{"id":125,"date":"2021-08-18T00:00:00","date_gmt":"2021-08-18T07:00:00","guid":{"rendered":""},"modified":"2025-06-25T03:42:41","modified_gmt":"2025-06-25T10:42:41","slug":"genomics-testing-on-the-iss-with-hpe-spaceborne-computer2-and-azure","status":"publish","type":"post","link":"https:\/\/azure.microsoft.com\/en-us\/blog\/genomics-testing-on-the-iss-with-hpe-spaceborne-computer2-and-azure\/","title":{"rendered":"Genomics testing on the ISS with HPE Spaceborne Computer-2 and Azure"},"content":{"rendered":"\n
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Thanks to the power of open source, the compute capability provided by the HPE Spaceborne Computer-2, and the scalability of Azure, we are empowering developers to build for space at a speed that\u2019s out of this world.\u201d\u2014<\/em>Kevin Mack, Senior Software Engineer, Microsoft<\/p>\n<\/blockquote>\n\n\n\n

This morning Microsoft News published a story<\/a> about the use of Azure, enabled by HPE\u2019s Spaceborne Computer-2<\/a> on the International Space Station (ISS). The project was designed to overcome the limited bandwidth between ISS and Earth by validating the benefits of a computational workflow that spans edge and cloud. Under this workflow, examination of high-volume raw data is processed and performed on the ISS using the HPE Spaceborne Computer-2\u2019s edge computing platform and a much smaller data set containing only \u201cinteresting bits\u201d is sent to Earth, where cloud resources are used to perform compute-intensive analysis to determine what those interesting bits really mean.<\/p>\n\n\n\n

The Azure Space team performed the software development needed for the entire experiment in just three days.<\/p>\n\n\n\n

A brief background<\/h2>\n\n\n\n

The International Space Station (ISS), a microgravity and space environment research laboratory, has just observed 20 years of continuous human presence. New technology is delivered to it regularly, as needed to keep up with the research being performed. Computers used on the ISS have typically been custom-built with specialized hardware and programming models, needed to deliver the reliability needed in space. Unfortunately, the developer experience for targeting these custom spaceborne systems is complex, making programming slow and challenging compared to the commercial-off-the-shelf systems used by most developers today.<\/p>\n\n\n\n

Installed in 2017, Spaceborne Computer-1, designed by HPE, validated that a modern, commercial-off-the-shelf computer could survive a launch into space, be installed by astronauts, and operate correctly on the ISS\u2014without \u201cflipping bits\u201d due to increased radiation in space. Basically, it was a year-long test to see if the computer hardware used on Earth would function normally in space. Building on this success, HPE\u2019s Spaceborne Computer-2, an edge computing platform with purposely designed features for harsh environments, was installed in April 2021 to deliver twice as much compute performance, and for the first time, artificial intelligence (AI) capabilities to advance space exploration and research by enabling the same programming models and developer experiences used on Earth.<\/p>\n\n\n\n

In many ways, Spaceborne Computer-2, which is comprised of the HPE Edgeline EL4000 Converged Edge system and HPE ProLiant DL360 Gen10 server, is the ultimate edge computing device platform, putting a game-changing amount of compute at the edge of space. However, the real limiting factor is the bandwidth between the ISS and Earth. Although Spaceborne Computer-2 supports the maximum available network speeds, it only receives from NASA an allocation of two hours of communication bandwidth a week to transmit data to earth, with a maximum download speed of 250 kilobytes per second.<\/p>\n\n\n\n

In some cases, working around limited bandwidth can be accomplished by HPE helping researchers to compress data on Spaceborne Computer-2 before sending it down to Earth. In other cases, the data can be fully analyzed in space without needing to use the slow downlink at all. But what about research that requires more compute or bandwidth than what Spaceborne Computer-2 can provide, or that can be allotted to a single experiment among many? To address such scenarios, HPE applied its vision for an \u201cedge to cloud\u201d experience, in which Spaceborne Computer-2 is used to perform preliminary analysis or filtering on large data sets, extract what\u2019s interesting or unexpected, and then burst those results down to Earth and into the public cloud for full analysis.<\/p>\n\n\n\n

The Azure Space experiment<\/h2>\n\n\n\n

The Azure Space team at Microsoft proposed an experiment that simulates how NASA might monitor astronaut health in the presence of increased radiation exposure, as exists outside of our protective atmosphere. Such exposure will only increase as astronauts venture beyond the ISS\u2019s low-earth orbit into and beyond the Van Allen Belts.<\/p>\n\n\n\n

The experiment assumes access to a gene sequencer onboard the ISS, which is used to regularly monitor blood samples from astronauts. However, gene sequencing can generate an incredible amount of data\u2014far too much for a 2Mbps\/sec downlink\u2014and the output needs to be compared against a large clinical database that\u2019s constantly being updated.<\/p>\n\n\n\n

To overcome those limitations, the experiment uses HPE Spaceborne Computer-2 to perform the initial process of comparing extracted gene sequences against reference DNA segments and capture only the differences, or mutations, which are then downloaded to the HPE ground station.<\/p>\n\n\n\n

On earth, the data is uploaded to Azure, where the Microsoft Genomics service does the computational \u201calignment\u201d work\u2014the process of matching the short base-pair gene sequence reads in the downloaded data (which are about 70 base pairs in length) against the full 3 giga-base-pair human genome, as required to determine where in the human genome each mutation is located and the type of change (deletion, addition, replication, or swap). Aligned reads are then checked against the National Institute for Health\u2019s dbSNP database to determine what the health impacts of a given mutation might mean. Watch the video below to see Azure in action.<\/p>\n\n\n\n

\"Genomics<\/figure>\n\n\n\n

Development process and computational workflow<\/h2>\n\n\n\n

The entire experiment was coded by 10 volunteers from the Azure Space team and its parent organization, the Azure Special Capabilities, Infrastructure, and Innovation Team. All major software components (both ISS-based and Azure-based) were written in Python and bash using Visual Studio Code, GitHub, and the Python libraries for Azure Functions and Azure Blob Storage. David Weinstein, Principal Software Engineering Manager at Azure Space, led the three-day development effort\u2014consisting of a one-day hackathon and two days of cleanup.<\/p>\n\n\n\n

The following graphic shows the computational workflow. It starts on the ISS, on Spaceborne Computer-2, which runs Red Hat Linux 7.4.<\/p>\n\n\n\n

\"Architecture<\/figure>\n\n\n\n

In space<\/h3>\n\n\n\n